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- EMDB-66599: B/Brisbane/60/2008 HA in complex with BP-1A -

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Basic information

Entry
Database: EMDB / ID: EMD-66599
TitleB/Brisbane/60/2008 HA in complex with BP-1A
Map data
Sample
  • Complex: B/Brisbane/60/2008 HA in complex with BP-1A antibody
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: BP-1A heavy chain
    • Protein or peptide: BP-1A light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / HA / antibody / influenza B virus / BP-1A / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Influenza B virus (B/Brisbane/60/2008)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsNguyen VHT / Ma C
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-IA-113-L02 Taiwan
Ministry of Science and Technology (MoST, Taiwan)NSTC 114-2320-B-001 -018 -MY3 Taiwan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Broad neutralization of influenza B hemagglutinin antibodies via receptor mimicry and glycan engagement.
Authors: Kuan-Ying A Huang / Hong Thuy Vy Nguyen / Yi-Yin Chen / Kai-Jung Wu / Po-Hsien Hsu / Yo-Min Liu / Tzou-Yien Lin / Che Ma /
Abstract: Influenza B virus contributes to seasonal influenza epidemics and causes global morbidity and mortality. The two antigenically distinct lineages, Victoria and Yamagata, cocirculate within the ...Influenza B virus contributes to seasonal influenza epidemics and causes global morbidity and mortality. The two antigenically distinct lineages, Victoria and Yamagata, cocirculate within the population and are subject to ongoing antigenic drift. In this study, we report the isolation of cross-lineage neutralizing anti-influenza B hemagglutinin (HA) monoclonal antibodies, exhibiting hemagglutination-inhibition activities, from vaccinated adult donors. While some antibodies exhibit reduced activities against recently emerged antigenic variants, BP-1A and BO-6B demonstrate broad neutralization across influenza B viruses isolated over the past two decades and confer protection in mice against lethal challenge from both lineages. Structural analysis of the antibody Fab domains in complex with HA reveals two distinct molecular binding modes: BP-1A uses a long heavy chain CDR3 loop that mimics the ligand to target the receptor-binding site, while BO-6B engages a conserved cleft on the surface of vestigial esterase subdomain through key interactions with glycan moieties. These findings elucidate the molecular basis for broad neutralization by human anti-influenza B HA antibodies and provide insights that may guide the development of immunotherapeutics and rational vaccine design.
History
DepositionOct 14, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66599.png

Downloads & links

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Map

FileDownload / File: emd_66599.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.227
Minimum - Maximum-3.840971 - 4.8551984
Average (Standard dev.)0.0008756021 (±0.07512495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66599_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66599_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : B/Brisbane/60/2008 HA in complex with BP-1A antibody

EntireName: B/Brisbane/60/2008 HA in complex with BP-1A antibody
Components
  • Complex: B/Brisbane/60/2008 HA in complex with BP-1A antibody
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: BP-1A heavy chain
    • Protein or peptide: BP-1A light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: B/Brisbane/60/2008 HA in complex with BP-1A antibody

SupramoleculeName: B/Brisbane/60/2008 HA in complex with BP-1A antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus (B/Brisbane/60/2008)
Molecular weightTheoretical: 39.285133 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MKAIIVLLMV VTSNADRICT GITSSNSPHV VKTATQGEVN VTGVIPLTTT PTKSHFANLK GTETRGKLCP KCLNCTDLDV ALGRPKCTG KIPSARVSIL HEVRPVTSGC FPIMHDRTKI RQLPNLLRGY EHIRLSTHNV INAENAPGGP YKIGTSGSCP N ITNGNGFF ...String:
MKAIIVLLMV VTSNADRICT GITSSNSPHV VKTATQGEVN VTGVIPLTTT PTKSHFANLK GTETRGKLCP KCLNCTDLDV ALGRPKCTG KIPSARVSIL HEVRPVTSGC FPIMHDRTKI RQLPNLLRGY EHIRLSTHNV INAENAPGGP YKIGTSGSCP N ITNGNGFF ATMAWAVPKN DKNKTATNPL TIEVPYICTE GEDQITVWGF HSDNETQMAK LYGDSKPQKF TSSANGVTTH YV SQIGGFP NQTEDGGLPQ SGRIVVDYMV QKSGKTGTIT YQRGILLPQK VWCASGRSKV IKGSLPLIGE ADCLHEKYGG LNK SKPYYT GEHAKAIGNC PIWVKTPLKL ANGTKYRPPA KLLKER

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus (B/Brisbane/60/2008)
Molecular weightTheoretical: 25.562551 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: GFFGAIAGFL EGGWEGMIAG WHGYTSHGAH GVAVAADLKS TQEAINKITK NLNSLSELEV KNLQRLSGAM DELHNEILEL DEKVDDLRA DTISSQIELA VLLSNEGIIN SEDEHLLALE RKLKKMLGPS AVEIGNGCFE TKHKCNQTCL DRIAAGTFDA G EFSLPTFD ...String:
GFFGAIAGFL EGGWEGMIAG WHGYTSHGAH GVAVAADLKS TQEAINKITK NLNSLSELEV KNLQRLSGAM DELHNEILEL DEKVDDLRA DTISSQIELA VLLSNEGIIN SEDEHLLALE RKLKKMLGPS AVEIGNGCFE TKHKCNQTCL DRIAAGTFDA G EFSLPTFD SLNITAASLN DDGLDNHTIL DIRSLVPRGS PGSGYIPEAP RDGQAYVRKD GEWVLLSTFL GHHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #3: BP-1A heavy chain

MacromoleculeName: BP-1A heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.144578 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSE VQLVESGGGV VQPGRSLRLS CAASGFIFND YNMHWVRQSP GKGLEWVATI WNDGSDKYYS DSVKGRFTI SKDDSKKTLF LQMNSLRAED TAVYYCARDE ISYWDYYGSG SLDHWGQGTL VTVSSASTKG PSVFPLAPSS K STSGGTAA ...String:
MGWSCIILFL VATATGVHSE VQLVESGGGV VQPGRSLRLS CAASGFIFND YNMHWVRQSP GKGLEWVATI WNDGSDKYYS DSVKGRFTI SKDDSKKTLF LQMNSLRAED TAVYYCARDE ISYWDYYGSG SLDHWGQGTL VTVSSASTKG PSVFPLAPSS K STSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DK KVEPKSC DKTHTCPPCP APELLGGPSV FLFPPKPKDT LMISRTPEVT CVVVDVSHED PEVKFNWYVD GVEVHNAKTK PRE EQYNST YRVVSVLTVL HQDWLNGKEY KCKVSNKALP APIEKTISKA KGQPREPQVY TLPPSRDELT KNQVSLTCLV KGFY PSDIA VEWESNGQPE NNYKTTPPVL DSDGSFFLYS KLTVDKSRWQ QGNVFSCSVM HEALHNHYTQ KSLSLSPGK

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Macromolecule #4: BP-1A light chain

MacromoleculeName: BP-1A light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.243191 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSE IVMTQSPATV SVSPGERATL SCRASQSVGS KLGWYQQKPG QAPRLLISGA STRASGIPAR FSGSGSGTD FTLTITSLQS EDFAVYYCQQ YDNWPRTFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String:
MGWSCIILFL VATATGVHSE IVMTQSPATV SVSPGERATL SCRASQSVGS KLGWYQQKPG QAPRLLISGA STRASGIPAR FSGSGSGTD FTLTITSLQS EDFAVYYCQQ YDNWPRTFGQ GTKVEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.30 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU (ver. 3.6.0.6389)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 8113 / Average electron dose: 46.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1823425
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6fyw

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 343055
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.5.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6fyw


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.10)
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9x5w:
B/Brisbane/60/2008 HA in complex with BP-1A

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